Per chromosome imputation report for cohort T1DGC_cohort.
Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.
Information captured during the processing of this cohort.
| Property | Value |
|---|---|
| FORMAT | MINIMAC2 |
| UPLOADED | 12.4.2021 |
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 20497001 | 81.568 |
| 0.1 | 1220470 | 4.857 |
| 0.2 | 811191 | 3.228 |
| 0.3 | 617949 | 2.459 |
| 0.4 | 494996 | 1.970 |
| 0.5 | 406341 | 1.617 |
| 0.6 | 350646 | 1.395 |
| 0.7 | 291635 | 1.161 |
| 0.8 | 243804 | 0.970 |
| 0.9 | 194727 | 0.775 |
| Total | 25128760 | 100.000 |
Variants binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 1268508 | 5.048 |
| 0.4 | 1503337 | 5.983 |
| 0.5 | 1965354 | 7.821 |
| 0.6 | 2654962 | 10.565 |
| 0.7 | 3458208 | 13.762 |
| 0.8 | 4034514 | 16.055 |
| 0.9 | 10192185 | 40.560 |
| 1.0 | 51692 | 0.206 |
| Total | 25128760 | 100.000 |
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1536531 | 81.6889 |
| 0.1 | 89911 | 4.7801 |
| 0.2 | 57738 | 3.0696 |
| 0.3 | 45509 | 2.4195 |
| 0.4 | 37536 | 1.9956 |
| 0.5 | 30270 | 1.6093 |
| 0.6 | 27360 | 1.4546 |
| 0.7 | 21974 | 1.1682 |
| 0.8 | 18589 | 0.9883 |
| 0.9 | 15536 | 0.8260 |
| Total | 1880954 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 98971 | 5.2617 |
| 0.4 | 116931 | 6.2166 |
| 0.5 | 149567 | 7.9517 |
| 0.6 | 201924 | 10.7352 |
| 0.7 | 264384 | 14.0558 |
| 0.8 | 308052 | 16.3774 |
| 0.9 | 737693 | 39.2191 |
| 1.0 | 3432 | 0.1825 |
| Total | 1880954 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1737956 | 82.2001 |
| 0.1 | 100876 | 4.7711 |
| 0.2 | 65593 | 3.1024 |
| 0.3 | 49851 | 2.3578 |
| 0.4 | 38518 | 1.8218 |
| 0.5 | 32920 | 1.5570 |
| 0.6 | 28768 | 1.3606 |
| 0.7 | 23263 | 1.1003 |
| 0.8 | 20210 | 0.9559 |
| 0.9 | 16344 | 0.7730 |
| Total | 2114299 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 103782 | 4.9086 |
| 0.4 | 121627 | 5.7526 |
| 0.5 | 160492 | 7.5908 |
| 0.6 | 219130 | 10.3642 |
| 0.7 | 291562 | 13.7900 |
| 0.8 | 344302 | 16.2845 |
| 0.9 | 868390 | 41.0722 |
| 1.0 | 5014 | 0.2371 |
| Total | 2114299 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1441882 | 81.5967 |
| 0.1 | 87668 | 4.9612 |
| 0.2 | 55347 | 3.1321 |
| 0.3 | 43084 | 2.4381 |
| 0.4 | 35180 | 1.9909 |
| 0.5 | 29118 | 1.6478 |
| 0.6 | 24728 | 1.3994 |
| 0.7 | 20347 | 1.1514 |
| 0.8 | 16994 | 0.9617 |
| 0.9 | 12735 | 0.7207 |
| Total | 1767083 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 84583 | 4.7866 |
| 0.4 | 100046 | 5.6616 |
| 0.5 | 132178 | 7.4800 |
| 0.6 | 181514 | 10.2720 |
| 0.7 | 241990 | 13.6943 |
| 0.8 | 288690 | 16.3371 |
| 0.9 | 733634 | 41.5167 |
| 1.0 | 4448 | 0.2517 |
| Total | 1767083 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1386722 | 80.6895 |
| 0.1 | 82142 | 4.7796 |
| 0.2 | 60783 | 3.5368 |
| 0.3 | 45277 | 2.6345 |
| 0.4 | 33857 | 1.9700 |
| 0.5 | 28032 | 1.6311 |
| 0.6 | 24432 | 1.4216 |
| 0.7 | 21800 | 1.2685 |
| 0.8 | 20149 | 1.1724 |
| 0.9 | 15397 | 0.8959 |
| Total | 1718591 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 86883 | 5.0555 |
| 0.4 | 100717 | 5.8604 |
| 0.5 | 131753 | 7.6663 |
| 0.6 | 177622 | 10.3353 |
| 0.7 | 229368 | 13.3463 |
| 0.8 | 269697 | 15.6929 |
| 0.9 | 719191 | 41.8477 |
| 1.0 | 3360 | 0.1955 |
| Total | 1718591 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1311159 | 81.7219 |
| 0.1 | 76716 | 4.7816 |
| 0.2 | 53094 | 3.3092 |
| 0.3 | 40002 | 2.4932 |
| 0.4 | 31533 | 1.9654 |
| 0.5 | 24557 | 1.5306 |
| 0.6 | 22449 | 1.3992 |
| 0.7 | 18435 | 1.1490 |
| 0.8 | 14780 | 0.9212 |
| 0.9 | 11690 | 0.7286 |
| Total | 1604415 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 77529 | 4.8322 |
| 0.4 | 91286 | 5.6897 |
| 0.5 | 119891 | 7.4726 |
| 0.6 | 164036 | 10.2240 |
| 0.7 | 216567 | 13.4982 |
| 0.8 | 260188 | 16.2170 |
| 0.9 | 671484 | 41.8523 |
| 1.0 | 3434 | 0.2140 |
| Total | 1604415 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1266410 | 80.9261 |
| 0.1 | 80893 | 5.1692 |
| 0.2 | 52860 | 3.3779 |
| 0.3 | 40412 | 2.5824 |
| 0.4 | 32630 | 2.0851 |
| 0.5 | 25689 | 1.6416 |
| 0.6 | 22585 | 1.4432 |
| 0.7 | 17140 | 1.0953 |
| 0.8 | 15416 | 0.9851 |
| 0.9 | 10861 | 0.6940 |
| Total | 1564896 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 71139 | 4.5459 |
| 0.4 | 83482 | 5.3347 |
| 0.5 | 108716 | 6.9472 |
| 0.6 | 150014 | 9.5862 |
| 0.7 | 203763 | 13.0209 |
| 0.8 | 246006 | 15.7203 |
| 0.9 | 697243 | 44.5552 |
| 1.0 | 4533 | 0.2897 |
| Total | 1564896 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1160183 | 81.5374 |
| 0.1 | 69020 | 4.8507 |
| 0.2 | 47809 | 3.3600 |
| 0.3 | 35310 | 2.4816 |
| 0.4 | 28731 | 2.0192 |
| 0.5 | 23423 | 1.6462 |
| 0.6 | 19271 | 1.3544 |
| 0.7 | 16523 | 1.1612 |
| 0.8 | 12101 | 0.8505 |
| 0.9 | 10513 | 0.7389 |
| Total | 1422884 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 70931 | 4.9850 |
| 0.4 | 84267 | 5.9223 |
| 0.5 | 109725 | 7.7115 |
| 0.6 | 147366 | 10.3569 |
| 0.7 | 195005 | 13.7049 |
| 0.8 | 229592 | 16.1357 |
| 0.9 | 583204 | 40.9875 |
| 1.0 | 2794 | 0.1964 |
| Total | 1422884 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1158266 | 82.3135 |
| 0.1 | 64353 | 4.5733 |
| 0.2 | 44659 | 3.1737 |
| 0.3 | 32120 | 2.2826 |
| 0.4 | 27540 | 1.9572 |
| 0.5 | 21624 | 1.5367 |
| 0.6 | 19123 | 1.3590 |
| 0.7 | 15687 | 1.1148 |
| 0.8 | 13368 | 0.9500 |
| 0.9 | 10399 | 0.7390 |
| Total | 1407139 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 68685 | 4.8812 |
| 0.4 | 81266 | 5.7753 |
| 0.5 | 104191 | 7.4045 |
| 0.6 | 142402 | 10.1200 |
| 0.7 | 188814 | 13.4183 |
| 0.8 | 226292 | 16.0817 |
| 0.9 | 591322 | 42.0230 |
| 1.0 | 4167 | 0.2961 |
| Total | 1407139 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 866945 | 81.7432 |
| 0.1 | 53648 | 5.0584 |
| 0.2 | 33821 | 3.1889 |
| 0.3 | 24975 | 2.3549 |
| 0.4 | 20403 | 1.9238 |
| 0.5 | 15858 | 1.4952 |
| 0.6 | 14677 | 1.3839 |
| 0.7 | 11910 | 1.1230 |
| 0.8 | 9444 | 0.8905 |
| 0.9 | 8891 | 0.8383 |
| Total | 1060572 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 49938 | 4.7086 |
| 0.4 | 58816 | 5.5457 |
| 0.5 | 77871 | 7.3424 |
| 0.6 | 107412 | 10.1277 |
| 0.7 | 143417 | 13.5226 |
| 0.8 | 173763 | 16.3839 |
| 0.9 | 447098 | 42.1563 |
| 1.0 | 2257 | 0.2128 |
| Total | 1060572 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 993849 | 81.3531 |
| 0.1 | 60620 | 4.9621 |
| 0.2 | 39646 | 3.2453 |
| 0.3 | 28716 | 2.3506 |
| 0.4 | 24491 | 2.0048 |
| 0.5 | 20895 | 1.7104 |
| 0.6 | 17170 | 1.4055 |
| 0.7 | 13817 | 1.1310 |
| 0.8 | 12845 | 1.0514 |
| 0.9 | 9599 | 0.7857 |
| Total | 1221648 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 57938 | 4.7426 |
| 0.4 | 68419 | 5.6005 |
| 0.5 | 89902 | 7.3591 |
| 0.6 | 122118 | 9.9962 |
| 0.7 | 161919 | 13.2541 |
| 0.8 | 195719 | 16.0209 |
| 0.9 | 523011 | 42.8119 |
| 1.0 | 2622 | 0.2146 |
| Total | 1221648 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 980869 | 81.2671 |
| 0.1 | 58975 | 4.8862 |
| 0.2 | 36448 | 3.0198 |
| 0.3 | 30686 | 2.5424 |
| 0.4 | 24302 | 2.0135 |
| 0.5 | 20869 | 1.7290 |
| 0.6 | 18004 | 1.4917 |
| 0.7 | 14215 | 1.1777 |
| 0.8 | 12166 | 1.0080 |
| 0.9 | 10435 | 0.8646 |
| Total | 1206969 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 57265 | 4.7445 |
| 0.4 | 68854 | 5.7047 |
| 0.5 | 89865 | 7.4455 |
| 0.6 | 124020 | 10.2753 |
| 0.7 | 166635 | 13.8061 |
| 0.8 | 198354 | 16.4341 |
| 0.9 | 499498 | 41.3845 |
| 1.0 | 2478 | 0.2053 |
| Total | 1206969 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 942631 | 81.4067 |
| 0.1 | 56746 | 4.9007 |
| 0.2 | 35506 | 3.0663 |
| 0.3 | 30489 | 2.6331 |
| 0.4 | 22948 | 1.9818 |
| 0.5 | 19080 | 1.6478 |
| 0.6 | 16133 | 1.3933 |
| 0.7 | 12803 | 1.1057 |
| 0.8 | 12294 | 1.0617 |
| 0.9 | 9298 | 0.8030 |
| Total | 1157928 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 57529 | 4.9683 |
| 0.4 | 68869 | 5.9476 |
| 0.5 | 90006 | 7.7730 |
| 0.6 | 122416 | 10.5720 |
| 0.7 | 158630 | 13.6995 |
| 0.8 | 182349 | 15.7479 |
| 0.9 | 475215 | 41.0401 |
| 1.0 | 2914 | 0.2517 |
| Total | 1157928 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 699713 | 80.5303 |
| 0.1 | 43052 | 4.9549 |
| 0.2 | 27668 | 3.1843 |
| 0.3 | 22774 | 2.6211 |
| 0.4 | 17409 | 2.0036 |
| 0.5 | 15651 | 1.8013 |
| 0.6 | 12474 | 1.4356 |
| 0.7 | 11313 | 1.3020 |
| 0.8 | 9765 | 1.1239 |
| 0.9 | 9063 | 1.0431 |
| Total | 868882 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 40391 | 4.6486 |
| 0.4 | 48364 | 5.5662 |
| 0.5 | 64340 | 7.4049 |
| 0.6 | 89214 | 10.2677 |
| 0.7 | 119441 | 13.7465 |
| 0.8 | 139969 | 16.1091 |
| 0.9 | 365275 | 42.0397 |
| 1.0 | 1888 | 0.2173 |
| Total | 868882 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 646118 | 81.7158 |
| 0.1 | 39059 | 4.9399 |
| 0.2 | 26281 | 3.3238 |
| 0.3 | 18132 | 2.2932 |
| 0.4 | 15216 | 1.9244 |
| 0.5 | 11937 | 1.5097 |
| 0.6 | 9969 | 1.2608 |
| 0.7 | 9180 | 1.1610 |
| 0.8 | 8006 | 1.0125 |
| 0.9 | 6791 | 0.8589 |
| Total | 790689 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 38524 | 4.8722 |
| 0.4 | 45580 | 5.7646 |
| 0.5 | 60670 | 7.6731 |
| 0.6 | 82798 | 10.4716 |
| 0.7 | 109586 | 13.8596 |
| 0.8 | 125331 | 15.8509 |
| 0.9 | 326750 | 41.3247 |
| 1.0 | 1450 | 0.1834 |
| Total | 790689 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 567361 | 81.5638 |
| 0.1 | 33223 | 4.7761 |
| 0.2 | 22437 | 3.2255 |
| 0.3 | 16751 | 2.4081 |
| 0.4 | 14286 | 2.0538 |
| 0.5 | 11830 | 1.7007 |
| 0.6 | 8924 | 1.2829 |
| 0.7 | 7997 | 1.1496 |
| 0.8 | 6527 | 0.9383 |
| 0.9 | 6268 | 0.9011 |
| Total | 695604 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 36500 | 5.2472 |
| 0.4 | 43460 | 6.2478 |
| 0.5 | 57267 | 8.2327 |
| 0.6 | 76337 | 10.9742 |
| 0.7 | 95918 | 13.7892 |
| 0.8 | 109882 | 15.7966 |
| 0.9 | 275047 | 39.5407 |
| 1.0 | 1193 | 0.1715 |
| Total | 695604 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 627186 | 81.9464 |
| 0.1 | 38084 | 4.9760 |
| 0.2 | 22538 | 2.9448 |
| 0.3 | 19195 | 2.5080 |
| 0.4 | 14481 | 1.8920 |
| 0.5 | 11956 | 1.5621 |
| 0.6 | 10855 | 1.4183 |
| 0.7 | 9395 | 1.2275 |
| 0.8 | 6849 | 0.8949 |
| 0.9 | 4822 | 0.6300 |
| Total | 765361 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 42878 | 5.6023 |
| 0.4 | 50858 | 6.6450 |
| 0.5 | 66610 | 8.7031 |
| 0.6 | 87749 | 11.4650 |
| 0.7 | 110683 | 14.4615 |
| 0.8 | 124618 | 16.2823 |
| 0.9 | 281207 | 36.7417 |
| 1.0 | 758 | 0.0990 |
| Total | 765361 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 544682 | 81.9660 |
| 0.1 | 29996 | 4.5139 |
| 0.2 | 23116 | 3.4786 |
| 0.3 | 15483 | 2.3299 |
| 0.4 | 13350 | 2.0090 |
| 0.5 | 11230 | 1.6899 |
| 0.6 | 9032 | 1.3592 |
| 0.7 | 7860 | 1.1828 |
| 0.8 | 5872 | 0.8836 |
| 0.9 | 3901 | 0.5870 |
| Total | 664522 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 39950 | 6.0118 |
| 0.4 | 47123 | 7.0913 |
| 0.5 | 61533 | 9.2597 |
| 0.6 | 80267 | 12.0789 |
| 0.7 | 98055 | 14.7557 |
| 0.8 | 106689 | 16.0550 |
| 0.9 | 230374 | 34.6676 |
| 1.0 | 531 | 0.0799 |
| Total | 664522 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 558934 | 81.1186 |
| 0.1 | 33655 | 4.8844 |
| 0.2 | 23636 | 3.4303 |
| 0.3 | 17675 | 2.5652 |
| 0.4 | 13916 | 2.0196 |
| 0.5 | 10842 | 1.5735 |
| 0.6 | 9486 | 1.3767 |
| 0.7 | 8094 | 1.1747 |
| 0.8 | 6651 | 0.9653 |
| 0.9 | 6144 | 0.8917 |
| Total | 689033 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 34412 | 4.9942 |
| 0.4 | 41282 | 5.9913 |
| 0.5 | 54101 | 7.8517 |
| 0.6 | 74408 | 10.7989 |
| 0.7 | 96358 | 13.9845 |
| 0.8 | 110728 | 16.0701 |
| 0.9 | 276533 | 40.1335 |
| 1.0 | 1211 | 0.1758 |
| Total | 689033 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 422577 | 80.7744 |
| 0.1 | 28984 | 5.5402 |
| 0.2 | 18999 | 3.6316 |
| 0.3 | 13261 | 2.5348 |
| 0.4 | 9752 | 1.8641 |
| 0.5 | 8675 | 1.6582 |
| 0.6 | 7159 | 1.3684 |
| 0.7 | 6064 | 1.1591 |
| 0.8 | 4505 | 0.8611 |
| 0.9 | 3181 | 0.6080 |
| Total | 523157 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 33034 | 6.3144 |
| 0.4 | 40283 | 7.7000 |
| 0.5 | 52204 | 9.9786 |
| 0.6 | 65538 | 12.5274 |
| 0.7 | 77403 | 14.7954 |
| 0.8 | 81502 | 15.5789 |
| 0.9 | 172909 | 33.0511 |
| 1.0 | 284 | 0.0543 |
| Total | 523157 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 448900 | 81.6759 |
| 0.1 | 27125 | 4.9353 |
| 0.2 | 18053 | 3.2847 |
| 0.3 | 13465 | 2.4499 |
| 0.4 | 11222 | 2.0418 |
| 0.5 | 8921 | 1.6231 |
| 0.6 | 7761 | 1.4121 |
| 0.7 | 5955 | 1.0835 |
| 0.8 | 4515 | 0.8215 |
| 0.9 | 3694 | 0.6721 |
| Total | 549611 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 29420 | 5.3529 |
| 0.4 | 35076 | 6.3820 |
| 0.5 | 46742 | 8.5046 |
| 0.6 | 61177 | 11.1310 |
| 0.7 | 77215 | 14.0490 |
| 0.8 | 86393 | 15.7189 |
| 0.9 | 212877 | 38.7323 |
| 1.0 | 711 | 0.1294 |
| Total | 549611 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 261202 | 80.3241 |
| 0.1 | 15945 | 4.9034 |
| 0.2 | 10347 | 3.1819 |
| 0.3 | 8982 | 2.7621 |
| 0.4 | 7142 | 2.1963 |
| 0.5 | 5864 | 1.8033 |
| 0.6 | 4976 | 1.5302 |
| 0.7 | 4405 | 1.3546 |
| 0.8 | 4099 | 1.2605 |
| 0.9 | 2223 | 0.6836 |
| Total | 325185 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 17795 | 5.4723 |
| 0.4 | 21001 | 6.4582 |
| 0.5 | 27410 | 8.4290 |
| 0.6 | 36678 | 11.2791 |
| 0.7 | 45973 | 14.1375 |
| 0.8 | 50188 | 15.4337 |
| 0.9 | 125794 | 38.6838 |
| 1.0 | 346 | 0.1064 |
| Total | 325185 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 266503 | 81.5178 |
| 0.1 | 15903 | 4.8644 |
| 0.2 | 11044 | 3.3781 |
| 0.3 | 7867 | 2.4064 |
| 0.4 | 6829 | 2.0889 |
| 0.5 | 5423 | 1.6588 |
| 0.6 | 4622 | 1.4138 |
| 0.7 | 4086 | 1.2498 |
| 0.8 | 2806 | 0.8583 |
| 0.9 | 1843 | 0.5637 |
| Total | 326926 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 18930 | 5.7903 |
| 0.4 | 23024 | 7.0426 |
| 0.5 | 29219 | 8.9375 |
| 0.6 | 37633 | 11.5112 |
| 0.7 | 45307 | 13.8585 |
| 0.8 | 49826 | 15.2408 |
| 0.9 | 122356 | 37.4262 |
| 1.0 | 631 | 0.1930 |
| Total | 326926 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 670422 | 83.5508 |
| 0.1 | 33876 | 4.2218 |
| 0.2 | 23768 | 2.9621 |
| 0.3 | 17933 | 2.2349 |
| 0.4 | 13724 | 1.7103 |
| 0.5 | 11677 | 1.4552 |
| 0.6 | 10688 | 1.3320 |
| 0.7 | 9372 | 1.1680 |
| 0.8 | 5853 | 0.7294 |
| 0.9 | 5099 | 0.6355 |
| Total | 802412 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 51501 | 6.4183 |
| 0.4 | 62706 | 7.8147 |
| 0.5 | 81101 | 10.1072 |
| 0.6 | 103189 | 12.8599 |
| 0.7 | 120215 | 14.9817 |
| 0.8 | 126384 | 15.7505 |
| 0.9 | 256080 | 31.9138 |
| 1.0 | 1236 | 0.1540 |
| Total | 802412 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering